PDB Short entry for 1DK3 HEADER TRANSFERASE 06-DEC-99 1DK3 TITLE REFINED SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF DNA POLYMERASE TITLE 2 BETA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE BETA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN, RESIDUES 1-87; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PRSET-8K KEYWDS DNA-BINDING, DEOXYRIBOSE 5'-PHOSPHATE LYASE, NUCLEOTIDYLTRANSFERASE, KEYWDS 2 TRANSFERASE EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR M.W.MACIEJEWSKI,R.PRASAD,D.-J.LIU,S.H.WILSON,G.P.MULLEN REVDAT 4 16-FEB-22 1DK3 1 REMARK REVDAT 3 24-FEB-09 1DK3 1 VERSN REVDAT 2 01-APR-03 1DK3 1 JRNL REVDAT 1 14-FEB-00 1DK3 0 JRNL AUTH M.W.MACIEJEWSKI,D.LIU,R.PRASAD,S.H.WILSON,G.P.MULLEN JRNL TITL BACKBONE DYNAMICS AND REFINED SOLUTION STRUCTURE OF THE JRNL TITL 2 N-TERMINAL DOMAIN OF DNA POLYMERASE BETA. CORRELATION WITH JRNL TITL 3 DNA BINDING AND DRP LYASE ACTIVITY. JRNL REF J.MOL.BIOL. V. 296 229 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 10656829 JRNL DOI 10.1006/JMBI.1999.3455 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.-J.LIU,R.PRASAD,S.H.WILSON,E.F.DEROSE,G.P.MULLEN REMARK 1 TITL THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE N-TERMINAL REMARK 1 TITL 2 DOMAIN OF DNA POLYMERASE BETA AND MAPPING OF THE SSDNA REMARK 1 TITL 3 INTERACTION INTERFACE REMARK 1 REF BIOCHEMISTRY V. 35 6188 1996 REMARK 1 REFN ISSN 0006-2960 REMARK 1 DOI 10.1021/BI952656O REMARK 1 REFERENCE 2 REMARK 1 AUTH D.-J.LIU,E.F.DEROSE,R.PRASAD,S.H.WILSON,G.P.MULLEN REMARK 1 TITL ASSIGNMENTS OF 1H, 15N, AND 13C RESONANCES FOR THE BACKBONE REMARK 1 TITL 2 AND SIDE CHAINS OF THE N-TERMINAL DOMAIN OF DNA POLYMERASE REMARK 1 TITL 3 BETA. DETERMINATION OF THE SECONDARY STRUCTURE AND TERTIARY REMARK 1 TITL 4 CONTACTS. REMARK 1 REF BIOCHEMISTRY V. 33 9537 1994 REMARK 1 REFN ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 4.3, X-PLOR 4.0 REMARK 3 AUTHORS : VARIAN (VNMR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE NMR RESTRAINTS INCLUDED 921 USEFUL NOE DETERMINED UPPER REMARK 3 DISTANCE REMARK 3 RESTRAINTS, 41 HYDROGEN BONDS, AND 135 PHI AND CHI TORSION ANGLE REMARK 3 RESTRAINTS. REMARK 3 STRUCTURES WERE CALCULATED IN THE PROGRAM DYANA USING TORSION REMARK 3 ANGLE DYNAMICS. REMARK 3 THE CALCULATION STARTED WITH 100 RANDOMIZED STRUCTURES. THE 50 REMARK 3 STRUCTURES WITH REMARK 3 THE LOWEST TARGET FUNCTION WERE THEN REFINED WITHIN XPLOR USING REMARK 3 SIMULATED REMARK 3 ANNEALING. THE 25 LOWEST ENERGY STRUCTURAL CONFORMERS WERE REMARK 3 SELECTED TO REMARK 3 REPRESENT THE ENSEMBLE.THE 25 REFINED STRUCTURAL CONFORMERS REMARK 3 DISPLAYED NO NOE REMARK 3 VIOLATIONS >0.3 ANGSTROMS AND NO DIHEDRAL ANGLE VIOLATIONS >3 REMARK 3 DEGREES. THE REMARK 3 MINIMIZED AVERAGE STRUCTURE WAS CALCULATED FROM THE MEAN POSITION REMARK 3 OF THE REMARK 3 COORDINATES FOR THE 25 STRUCTURAL CONFORMERS AND WAS REFINED BY REMARK 3 POWELL ENERGY REMARK 3 MINIMIZATION IN XPLOR USING FULL NMR RESTRAINTS. REMARK 4 REMARK 4 1DK3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-DEC-99. REMARK 100 THE DEPOSITION ID IS D_1000010148. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300; 298 REMARK 210 PH : 6.7; 6.8 REMARK 210 IONIC STRENGTH : 400; 100 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 2.8 MM RAT DNA POLYMERASE BETA N REMARK 210 -TERMINAL DOMAIN (2-87) U-15N, REMARK 210 13C; 5MM TRIS- D11; 400MM NACL; REMARK 210 2 MM RAT DNA POLYMERASE BETA N- REMARK 210 TERMINAL DOMAIN (2-87) U-15N; REMARK 210 5MM TRIS-D11; 100MM NACL; 4 MM REMARK 210 RAT DNA POLYMERASE BETA N- REMARK 210 TERMINAL DOMAIN (2-87) U-15N; REMARK 210 5MM TRIS-D11; 400MM NACL; 2.8 MM REMARK 210 RAT DNA POLYMERASE BETA N- REMARK 210 TERMINAL DOMAIN (2-87) U-15N,13C; REMARK 210 5MM TRIS- D11; 400MM NACL; 1.4 REMARK 210 MM RAT DNA POLYMERASE BETA N- REMARK 210 TERMINAL DOMAIN (2-87); 5MM TRIS- REMARK 210 D11; 400MM NACL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 3D_13C- REMARK 210 SEPARATED_NOESY; HMQC-J REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : GN500; UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : GE; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 95, XEASY 1.3.13, DYANA REMARK 210 1.5 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS AND REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: REMARK 210 PROTEOLYTIC PROCESSING REMOVES THE N-TERMINAL MET IN A BACTERIAL REMARK 210 EXPRESSION REMARK 210 SYSTEM (SEE KUMAR ET AL., (1990) J. BIOL. CHEM. 265, 2124-2131). REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 2 99.50 60.10 REMARK 500 LYS A 3 -40.85 84.83 REMARK 500 LEU A 11 -72.79 -89.60 REMARK 500 ASN A 12 44.28 -104.73 REMARK 500 SER A 30 -70.48 -77.27 REMARK 500 ALA A 32 57.26 -150.81 REMARK 500 ALA A 78 -79.46 -61.80 REMARK 500 ARG A 83 -179.31 -63.43 REMARK 500 LYS A 84 34.78 -98.54 REMARK 500 GLU A 86 34.51 -98.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BNO RELATED DB: PDB REMARK 900 THIS IS THE PREVIOUS MINIMIZED AVERAGE STRUCTURE. REMARK 900 RELATED ID: 1BNP RELATED DB: PDB REMARK 900 THIS IS A PREVIOUS GROUP OF 55 STRUCTURAL CONFORMERS. DBREF 1DK3 A 1 87 UNP P06766 DPOB_RAT 1 87 SEQRES 1 A 87 MET SER LYS ARG LYS ALA PRO GLN GLU THR LEU ASN GLY SEQRES 2 A 87 GLY ILE THR ASP MET LEU VAL GLU LEU ALA ASN PHE GLU SEQRES 3 A 87 LYS ASN VAL SER GLN ALA ILE HIS LYS TYR ASN ALA TYR SEQRES 4 A 87 ARG LYS ALA ALA SER VAL ILE ALA LYS TYR PRO HIS LYS SEQRES 5 A 87 ILE LYS SER GLY ALA GLU ALA LYS LYS LEU PRO GLY VAL SEQRES 6 A 87 GLY THR LYS ILE ALA GLU LYS ILE ASP GLU PHE LEU ALA SEQRES 7 A 87 THR GLY LYS LEU ARG LYS LEU GLU LYS HELIX 1 1 GLY A 14 VAL A 29 1 16 HELIX 2 2 ILE A 33 LYS A 48 1 16 HELIX 3 3 SER A 55 LYS A 61 1 7 HELIX 4 4 THR A 67 THR A 79 1 13 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000